OBJECTIVE: To determine the perinatal predictors of discordant screening outcomes based on a two-stage screening protocol with transient-evoked otoacoustic emissions (TEOAE) and automated auditory brainstem response (AABR).METHODS: A cross-sectional study of infants tested with TEOAE and AABR under a hospital-based universal newborn hearing screening program in Lagos, Nigeria. Maternal and infant factors associated with discordant TEOAE and AABR outcomes were determined with multivariable logistic regression analyses adjusting for potential confounding factors.RESULTS: Of the 4718 infants enrolled under the program 1745 (36.9%) completed both TEOAE and AABR. Of this group, 1060 (60.7%) passed both TEOAE and AABR ("true-negatives"); 92 (5.3%) failed both TEOAE and AABR ("true-positive"); 571 (32.7%) failed TEOAE but passed AABR ("false-positives") while 22 (1.3%) passed TEOAE but failed AABR ("false-negatives"). Infants with false-positives were likely to be admitted into well-baby nursery (p=0.001), belong to mothers who attended antenatal care (p=0.010) or who delivered vaginally (p<0.001) compared to infants with true-negatives while infants with true-positives were also more likely to be delivered vaginally (p=0.002) or admitted into well-baby nursery (p=0.035) compared to infants with false-negatives. Infants with true-positives were significantly more likely to be delivered vaginally (p<0.001) and have severe hyperbilirubinemia (p=0.045) compared with infants with true-negatives. No association was observed between false-negatives and true-negatives. Antenatal care status, mode of delivery and nursery type were useful predictors of discordant outcomes among all infants undergoing screening (c-statistic=0.73).CONCLUSIONS: Given the available screening technologies, discordant TEOAE and AABR may be inevitable for some categories of hearing loss among apparently healthy newborns whose mothers received prenatal care. The potential limitations of perinatal morbidities as basis of targeted screening for such cases therefore merit further consideration.